I lecture Biochemistry at a small University in Oporto. Although originally raised as an experimental Biochemist, I have since changed my research into theoretical and computational chemistry and biochemistry. In this blog, I will mostly commment on recent (or not so recent...) research papers that happen to have called my attention. I hope someone will find it interesting/useful :-)

Wednesday, July 8, 2015

Gamess (US) frequently asked questions. Part 7: How to distinguish alpha from beta orbitals in the $VEC deck

Each line in a $VEC group contains the coefficients of five basis
functions for a given orbital. These are formatted in a special way,
with seven numbers in each line. These numbers are:

1st) the
number of the orbital to which the coefficients belong (written with at
most two characters, so that 1 means orbital 1, .. , 99 means orbital
99, 00 means orbital 100) . This number is repeated in the beginning of
every line, until all coefficients for that orbital have been written

2nd)
this number tells the program how to assign the coefficients to the
basis functions. "1" means that the coefficients are for basis functions
1-5, "2" means that the coefficients are for basis functions 5-10, etc.
In general , that number "n" directs the program to assign the five
coefficients present in the line to basis functions 5*(n-1)+1 to 5*n.

3rd to 7th) coefficients of five basis functions

BETA orbitals are punched as a group immediately after all ALPHA orbitals.

This
format entails that in molecules with more than 100 orbitals the $VEC
group contains several blocks with the same 1st number. For example, in a
molecule with 200 orbitals, alpha orbital 27 is described by the first
block of lines beginning with "27", and alpha orbital 127 is described
by the SECOND block of lines beginning with "27".

I usually find
the beginning of the BETA orbitals by repeating a search for the string "
1 1" : if that string is preceded by a block beginning with "00 1", it
usually refers to orbitals 101, or 201, etc. (the exception being those
systems with exactly 100, 200, etc. orbitals). If string " 1 1" is NOT
preceded by a block beginning with "00 1", you are sure to have found
the beginnning of the BETA orbitals